Contacts of the helix formed by residues 391 - 401 (chain A) in PDB entry 3U44
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LEU* 6.1 2.0 - - - -
378A ILE 2.6 25.8 + - - -
379A LEU* 2.8 19.3 + - - -
381A ALA* 3.4 37.2 - - - +
389A GLU* 3.1 6.7 + - - -
390A PRO* 1.3 81.5 - - - +
392A GLU* 1.3 62.0 + - - +
393A ALA* 3.0 8.6 + - - +
394A ALA 2.9 16.8 + - - -
395A ARG* 2.9 11.4 + - - +
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Residues in contact with GLU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 4.8 3.1 + - + -
123A LEU* 5.1 16.4 - - + +
391A SER* 1.3 72.4 - - - +
393A ALA* 1.3 64.8 + - - +
395A ARG* 3.4 34.7 - - - +
396A PHE* 3.4 18.4 + - - +
153B ARG* 2.5 52.3 + - + +
157B VAL* 4.2 9.5 - - - +
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Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 3.8 32.8 - - + -
123A LEU* 4.3 4.9 - - + -
378A ILE* 3.8 27.8 - - + +
379A LEU* 4.4 3.6 - - + -
391A SER* 3.0 10.9 + - - +
392A GLU* 1.3 79.7 - - - +
394A ALA* 1.3 65.3 + - - +
396A PHE* 3.1 11.6 + - - +
397A TYR* 3.1 21.8 - - - -
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A LEU* 3.4 17.6 - - - +
390A PRO* 3.8 12.8 - - + -
391A SER* 2.9 11.6 + - - +
393A ALA* 1.3 79.7 - - - +
395A ARG* 1.3 63.0 + - - +
397A TYR* 3.1 7.4 + - - +
398A GLN* 3.0 27.3 + - - +
422A LEU* 3.1 41.1 - - + +
423A VAL* 5.8 0.2 - - - -
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Residues in contact with ARG 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A GLU* 4.5 15.8 + - - +
390A PRO* 3.4 20.6 + - + +
391A SER* 2.9 9.2 + - - +
392A GLU* 3.4 32.9 - - - +
394A ALA* 1.3 77.0 - - + +
396A PHE* 1.3 62.7 + - - +
398A GLN* 3.3 16.6 + - - +
399A GLU* 3.0 24.1 + - - +
153B ARG* 4.9 11.7 - - - +
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Residues in contact with PHE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS* 3.0 27.1 - - - -
120A TYR* 3.5 20.9 - - - +
392A GLU 3.4 8.7 + - - +
393A ALA 3.1 9.5 + - - +
394A ALA 3.1 0.6 - - - -
395A ARG* 1.3 79.1 - - - +
397A TYR* 1.3 78.5 + + - +
399A GLU* 3.3 10.6 + - + +
400A GLN* 2.9 66.5 + - + +
627B ASP* 3.9 20.6 - - - -
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Residues in contact with TYR 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.8 20.0 - + - -
115A GLN* 4.5 2.9 + - + +
116A VAL* 3.4 36.0 + - + +
119A LYS* 4.0 8.3 - - - +
120A TYR* 3.6 33.8 - + - -
379A LEU* 4.2 12.8 - - + -
393A ALA 3.1 21.5 + - - -
394A ALA 3.1 6.0 + - - +
396A PHE* 1.3 90.9 - + - +
398A GLN* 1.3 61.5 + - - +
400A GLN* 4.1 8.3 - - - -
401A PHE* 2.9 64.9 + + + +
423A VAL* 3.9 15.2 - - + +
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Residues in contact with GLN 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A PRO* 4.3 21.0 - - - +
394A ALA* 3.0 21.9 + - - +
395A ARG* 3.6 14.7 - - - +
396A PHE 3.3 0.2 - - - -
397A TYR* 1.3 75.6 - - - +
399A GLU* 1.3 62.8 + - - +
401A PHE 3.2 16.7 - - - +
421A GLN 5.0 0.6 + - - -
422A LEU* 2.8 28.3 + - - +
423A VAL 3.6 15.7 - - - +
424A THR 3.8 12.6 + - - +
425A SER* 3.5 28.6 + - - -
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Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.2 29.0 + - - -
395A ARG 3.0 13.9 + - - +
396A PHE* 3.4 14.1 - - + +
398A GLN* 1.3 78.5 - - - +
400A GLN* 1.3 65.3 + - - +
401A PHE 3.6 0.2 + - - -
402A HIS* 4.2 8.5 + - - -
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Residues in contact with GLN 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASP* 3.9 20.3 + - - +
59A ARG* 2.7 41.3 + - - +
396A PHE* 2.9 51.3 + - + +
397A TYR* 3.3 10.4 + - - +
399A GLU* 1.3 80.7 - - + +
401A PHE* 1.3 78.2 + - + +
627B ASP* 4.9 6.5 + - - -
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Residues in contact with PHE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASP 4.5 5.2 - - - -
59A ARG 3.1 7.0 - - - +
60A LEU* 3.4 15.0 - - - -
61A LEU* 3.3 41.5 - - + -
105A SER* 3.1 29.4 - - - -
112A PHE* 3.9 8.5 - + - -
397A TYR* 2.9 59.4 + + + +
398A GLN* 3.2 13.7 - - - +
399A GLU 4.3 0.2 - - - +
400A GLN* 1.3 89.3 - - + +
402A HIS* 1.3 61.3 + - - +
403A GLU 4.0 11.0 - - - +
404A VAL* 4.2 9.4 - - + -
423A VAL* 4.6 6.5 - - + +
425A SER* 4.3 0.2 + - - -
432A ASN* 3.2 16.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il